ABSTRACT The Analytical and Metabolomic Core of the Case-MMPC specializes in the use of stable isotopes, mass spectrometry and metabolomics to investigate the regulation of pathways of intermediary metabolism in vivo and ex vivo. What makes our approach unique is the emphasis on quantitative measurements of inter-organ and intra-organ carbon fluxes using isotopomer analysis and mass spectrometry applications. We work with investigators to develop a research strategy that will appropriately address their hypotheses. Our strategy links clinical-type studies (limited to body fluids) and pure biochemical studies (such as the kinetics of purified enzymes). The association of metabolomics and mass isotopomer analysis provides a wealth of information on the regulation of known pathways. It also allows us to identify new pathways. Metabolomics was developed initially as a non-targeted strategy aimed at gathering sufficient data on a (patho)physiological process (biomarkers), so that one could formulate hypotheses to be tested. A variant of this strategy is to target metabolomic studies to classes of compounds and their concentrations and labeling patterns, which can provide much new information. We concentrate on the profiling of citric acid cycle intermediates, (hydroxy)acids, acyl-CoA esters, lipids and amino acids. The Case-MMPC complements the expertise of the other centers: Vanderbilt, Yale, Cincinnati, and UC Davis, through referrals and specialized working groups. The development of novel analytical strategies will enable the Core to offer (i) new assays that focus on measuring biomarkers of inflammation and oxidative stress, and (ii) custom synthesis of substrates labeled with stable isotopes.